The overall wealth of a society will have an important influence on this relationship. In a poor society, merchants will not be likely to be rich, and they will not be able to afford any regular thievery. They will not be able to bear such losses without going bankrupt. Here, merchants will fight tooth and nail to minimize the depredations of thieves. In richer lands, a little "stock loss" (among other things) can be tolerated rather better.
Alignment will somewhat modify this. In chaotic and/or evil societies which are rich, merchants may be very greedy, and may take many measures against thieves out of a love of money, not out of a need to survive. There may also be an important element of pride in a society which stresses individualism (chaotic) rather than one where merchants form groups, ally with each other, and try to regulate business practices (lawful). Over-proud merchants may resent monies or goods being stolen not primarily because of the loss of value—it may be negligible—but because of the loss of face. This can be an important factor in merchants putting pressure on authorities to suppress thieves, and in their hiring PCs for sums which exceed the value of their stolen goods!
Warfare[]
The merchants hate and fear the thieves. They go to extreme lengths to protect their property, and many able-bodied folk get jobs as nightwatchmen. Even ordinary warehouses have traps and many secret hidey-holes, wall safes and the like, and some have magical traps as well. Merchants often have bodyguards, and they won't pay protection monies. They may even band together to form mutual "insurance policies" to help each other. The merchants exert all their political clout to get the authorities to suppress thieves. Even small-scale pilferage will result in an offender being dragged off to face the sternest justice the merchant's advocate can plead for.
Under these circumstances, the thieves' guild may react in a number of ways. It may turn to other forms of crime. It may turn to imported help to crack the merchants (more thugs for protection racketeering, more thieves for daring robberies recruited from a friendly guild from a nearby town). It may use methods such as abductions and blackmail to force its way back into a position of strength. A really powerful guild will effectively "declare war" on the merchants if it thinks that forcing a few to cave in will lead to other merchants giving in also. Many options exist. This situation is a real struggle of wills, and the life of a thief will be dangerous—but never dull.
Opposition[]
Somewhat like the state of affairs described above, but the merchants don't go to such lengths to protect themselves or keep thieves off their backs. They don't like thieves, they don't accept them as a part of society or a tolerable evil, but they don't go overboard about them either. Such merchants are fairly stoutly resistant to any attempt at coercion or blackmail, and they use their influence with the powers-that-be to keep life tough for thieves.
Standoff[]
This is a fairly common state of affairs. The merchants don't like thieves, but they are somewhat fatalistic about them. A strong element of pragmatism influences their attitudes. If it loses them less to pay protection money than to suffer the thievery they would otherwise have to tolerate, they will pay up. This is a major difference from the oppositional state, where merchants will actually suffer extra loss rather than connive with thieves.
Merchants in a standoff will do what they can to get by. Unless thievery gets wildly out of hand, they won't get up in arms, and they will pay off thieves, or accept a certain level of theft, as they must.
Submission[]
This is a rare case. Here, the merchants are running scared. Coercion is rife; merchants pay a lot of money to avoid being robbed or having their homes burned down. Their profits may be almost all eaten away by this. The law is of little help, usually because it is corrupt, maybe because it is ineffectual. Thieves will have many spies in the midst of the merchants. This is an unstable state of affairs; it cannot persist long. Either the commercial life of the society falls apart, or the picture changes—often to Infiltration as described below.
Infiltration[]
Here, thieves have so many dealings with merchants that they actually start to get involved in commerce directly. This often happens as a natural evolution from either a standoff or a submission relationship. Thieves start to become merchants. They may have been spies in merchants employ before, they may "take over" the businesses of merchants they have bankrupted or driven off, or they may enter businesses their talents suit them for (e.g., as locksmiths, gem-cutters, moneylenders, pawnbrokers, and the like).
This has several attractions for the thief. First, additional income can be produced. Second, the business can be a simple exploitation of a skill or proficiency the thief already has. Third, it can provide a good cover for a thief. Fourth, there may be a more nefarious motive or two ("Ah, sir wants a combination lock which will be absolutely thief-proof! I have just the thing . . ."; why shouldn't a locksmith have the best lockpicks in town when apprehended by the constables down a dark alleyway at night?
At its most extreme, thieves can actually come to dominate commercial life, or at least to play a major role in it. Organized crime becomes big business. The thieves may even become important figures in society, and have political power. The City of Greyhawk is one notable example of this.
Complex/Mix[]
Again, examples of complicated or tense, oppositional relationships can easily be developed by the DM from the examples above. One group of merchants could be trying desperately to fend off thievery, while a second faction argues for accommodating thieves and paying them off. This leads to a major schism, with the more principled merchants accusing the pragmatists of collusion with crime; insults start to fly, then a few fists, then somebody's warehouse suffers a small fire . . . Involving the PCs in what will fast become a triangular conflict (two sets of merchants at each other's throats with the thieves gleefully picking up the spoils from anyone they can get at) leads to endless adventure possibilities.